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Structure paper

TitleStructural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance.
Journal, issue, pagesJ Mol Biol, Vol. 430, Issue 17, Page 2677-2687, Year 2018
Publish dateAug 17, 2018
AuthorsSimone Pellegrino / Natalia Demeshkina / Eder Mancera-Martinez / Sergey Melnikov / Angelita Simonetti / Alexander Myasnikov / Marat Yusupov / Gulnara Yusupova / Yaser Hashem /
PubMed AbstractOne of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a ...One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.
External linksJ Mol Biol / PubMed:29886014
MethodsEM (single particle)
Resolution3.9 - 4.4 Å
Structure data

0047

6gq1

EMDB-0047, PDB-6gq1:
Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin)
Method: EM (single particle) / Resolution: 4.4 Å

0048

6gqb

EMDB-0048, PDB-6gqb:
Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)
Method: EM (single particle) / Resolution: 3.9 Å

0049

6gqv

EMDB-0049, PDB-6gqv:
Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-0055:
Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin): SSU-focused map
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SO1:
[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • Baker's yeast (brewer's yeast)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsRIBOSOME / Eukaryotic 80S riboosme / mRNA-tRNA translocation / diphthamide / Eukaryotic 80S ribosome / eEF2 / translation fidelity

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